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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Spectrophotometric determination of metoclopramide hydrochloride in pharmaceutical tablets, by diazotization-coupling method with 1-naphthol as the coupling agent
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Simple, rapid and sensitive spectrophotometric method was proposed for the analysis of metoclopramide hydrochloride (MPH) in pure form as well as in pharmaceutical tablets. The method is based on the diazotization reaction of MPH with sodium nitrite in hydrochloric acid medium to form diazonium salt, which is coupled with 1-naphthol in sodium hydroxide medium to form azo dye, showing absorption maxima at 550 nm. Beer’s law is obeyed in the concentration range of 0.4 – 18 µg mL-1 of MPH with detection limit 0.5448 µg mL-1. The molar absorptivity and Sandell’s sensitivity are 3.4969 × 104 L mol-1 cm-1 and 0.0101 µg cm-2, respectively. The method was successfully applied to the determination of MPH in pharmaceutical tablets with

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Publication Date
Tue Dec 31 2019
Journal Name
Journal Of Engineering
A High Resolution 3D Geomodel for Giant Carbonate Reservoir- A Field Case Study from an Iraqi Oil Field
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Constructing a fine 3D geomodel for complex giant reservoir is a crucial task for hydrocarbon volume assessment and guiding for optimal development. The case under study is Mishrif reservoir of Halfaya oil field, which is an Iraqi giant carbonate reservoir. Mishrif mainly consists of limestone rocks which belong to Late Cenomanian age. The average gross thickness of formation is about 400m. In this paper, a high-resolution 3D geological model has been built using Petrel software that can be utilized as input for dynamic simulation. The model is constructed based on geological, geophysical, pertophysical and engineering data from about 60 available wells to characterize the structural, stratigraphic, and properties distribution along

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Publication Date
Tue Dec 31 2019
Journal Name
Journal Of Engineering
A High Resolution 3D Geomodel for Giant Carbonate Reservoir- A Field Case Study from an Iraqi Oil Field
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Constructing a fine 3D geomodel for complex giant reservoir is a crucial task for hydrocarbon volume assessment and guiding for optimal development. The case under study is Mishrif reservoir of Halfaya oil field, which is an Iraqi giant carbonate reservoir. Mishrif mainly consists of limestone rocks which belong to Late Cenomanian age. The average gross thickness of formation is about 400m. In this paper, a high-resolution 3D geological model has been built using Petrel software that can be utilized as input for dynamic simulation. The model is constructed based on geological, geophysical, pertophysical and engineering data from about 60 available wells to characterize the structural, stratigraphic, and properties distri

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Publication Date
Wed Jun 29 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Study the Activity of some plant resources as natural antioxidant: Study the Activity of some plant resources as natural antioxidant
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This study was done to test the activity of some plant extracts as antioxidant agents. The plants were (Morus rubra, Hibiscus sabdariffa L ., Rhus coriaria L., Anethum graveolens and Petroselinum sativum).
Ethanolic 98% (24 hours/ 25˚c) and distilled water (30 minutes/ 25˚c have been used for extraction.The Total phenols, total flavonoids, total anthocyanin, antioxidant activities were studied.
The extract of Morus rubra was chosen because it has a higher antioxidant activity.
The phenolic extract of Morus rubra was prepare and examined by application it in burger . The antioxidant activity test of Morus rubra was made before and after 3,6 days of cold storage. The sensory evaluation of all treatments were done within 5,1

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Publication Date
Wed Sep 01 2021
Journal Name
Journal Of Engineering
Spike neural network as a controller in SDN network
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The paper proposes a methodology for predicting packet flow at the data plane in smart SDN based on the intelligent controller of spike neural networks(SNN). This methodology is applied to predict the subsequent step of the packet flow, consequently reducing the overcrowding that might happen. The centralized controller acts as a reactive controller for managing the clustering head process in the Software Defined Network data layer in the proposed model. The simulation results show the capability of Spike Neural Network controller in SDN control layer to improve the (QoS) in the whole network in terms of minimizing the packet loss ratio and increased the buffer utilization ratio.

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Publication Date
Sat Dec 30 2023
Journal Name
Al-kindy College Medical Journal
A Large Anterior Urethral Calculus Presenting as Urethrocutaneous Fistula
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Presentation of urinary calculus ranges from painful urination to acute retention. Diagnosed by x-ray pelvis and non-contrast CT and removal of stone by various methods is the management. Variety in symptoms, sometimes make clinical diagnosis difficult until radiological investigations confirm it. In this case presentation, initial diagnosis was made of Urethrocutaneous fistula may be due to distal stricture, but on investigating, he was diagnosed as urethral calculus in urethral diverticulum , as the reason for his symptoms

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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Analyzing indicators of the results of applying forecasting methods for production plans (A case study at the Diyala State Company for Electrical Industries)
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Economic organizations operate in a dynamic environment, which necessitates the use of quantitative techniques to make their decisions. Here, the role of forecasting production plans emerges. So, this study aims to the analysis of the results of applying forecasting methods to production plans for the past years, in the Diyala State Company for Electrical Industries.

The Diyala State Company for Electrical Industries was chosen as a field of research for its role in providing distinguished products as well as the development and growth of its products and quality, and because it produces many products, and the study period was limited to ten years, from 2010 to 2019. This study used the descriptive approa

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Publication Date
Mon Feb 14 2022
Journal Name
Journal Of Educational And Psychological Researches
The Educational dimensions of children's television programs in the light of the universal rights of child
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The research aims at determining the type of educational dimensions to be broadcasted in children's television programs, clarifying the technical forms used in children's TV programs, analyzing the educational dimensions provided by children's television programs, and studying the educational dimensions of children's television programs. The researcher used a sample of children's programs: all of us heroes, which is a daily program on the mbc3 channel as well as the program of Tel flowers on the Algerian channel. The researcher designed an analysis content form included categories of analysis. Spss program was used to process the collected data. The research reached several results; the concentration of educational dimensions in

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Publication Date
Sun Nov 01 2020
Journal Name
Iraqi Journal Of Laser
Treatment of Striae Grvidarum as a Type of Striae Distensae Using Long Pulsed Nd:YAG Laser (1064nm) and Fractional CO2 Laser (10600nm)
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Striae distensae SD or stretch mark are frequent skin lesion that cause considerable aesthetic concern. The 1064nm long pulsed Nd:YAG Laser has been used to promote an increase in dermal collagen and is known to be a Laser that has a high affinity to vascular chromphores. Also by using fractional CO2 Laser 10600nm as an effective modality in treatment of striae distensae SD. It works to stimulate fibroblast and enhance Collagen formation, which is important for newly generated skin tissue.

Objectives: This study aims to verify the efficacy of long pulsed Nd: YAG Laser (1064nm) in the treatment of immature striae distensae (SD) and the efficacy of C02 fractional Laser (10600nm) in treatment o

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The role of investment climate indicators in stimulating economic growth: a standard study For Malaysia 1990-2016
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In globalization, the world became open area to competition for the attractive of investment, and the abilities of each country to win the confidence of investors depend upon the preparation to optimize circumstances.   The competitiveness is an essential means of expanding the capacity of developed to coexist in an international environment characterized by globalization. While competition describes the market structure, the behavior of investors and business, competitiveness is interested in the evaluation of business performance or countries and compare them in the conditions of competition available in these markets. Regarding Malaysia, which is depend on FDI-Export- Led Growth strategy,  it has taking on diffe

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